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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("flowWorkspace")
In most cases, you don't need to download the package archive at all.
flowWorkspace
Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore
Bioconductor version: 2.14
This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.
Author: Greg Finak, Mike Jiang
Maintainer: Greg Finak <gfinak at fhcrc.org>,Mike Jiang <wjiang2 at fhcrc.org>
Citation (from within R,
enter citation("flowWorkspace")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("flowWorkspace")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("flowWorkspace")
| R Script | Importing flowJo Workspaces into R | |
| Reference Manual | ||
| Text | NEWS | |
| Text | INSTALL |
Details
| biocViews | DataImport, DataRepresentation, FlowCytometry, Preprocessing, Software |
| Version | 3.10.09 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | Artistic-2.0 |
| Depends | R (>= 2.16.0), flowCore, flowViz, ncdfFlow, gridExtra |
| Imports | Biobase, BiocGenerics, graph, graphics, lattice, methods, stats, stats4, utils, RBGL, graph, XML, Biobase, IDPmisc, Cairo, tools, hexbin, gridExtra, Rgraphviz, data.table, plyr, latticeExtra, Rcpp |
| Suggests | testthat, flowWorkspaceData, RSVGTipsDevice |
| System Requirements | |
| URL | |
| Depends On Me | flowStats, openCyto, QUALIFIER |
| Imports Me | QUALIFIER |
| Suggests Me | COMPASS |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | flowWorkspace_3.10.09.tar.gz |
| Windows Binary | flowWorkspace_3.10.09.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | flowWorkspace_3.10.09.tgz |
| Mac OS X 10.9 (Mavericks) | flowWorkspace_3.10.09.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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